The map tracer is fine and accurate, it does do cell merging that is if you are say at 850rpm
it may use the values for 400-800 and 800-1200 and do an average between the two cells.
Map tracer can only show you one cell so it simply shows you one call. This is more obvious with datalogit as it shows crossing of the load points.
The base timing is 15 deg but the hand controller may show 20deg on the IGN map.
If you are referring to the idle IGN timing that can't be adjusted and whatever value is at 2x2 is ignored by base idle.
Whilst its possible that for one day you may not be able to replicate the knocking/misfiring and another you can its a case of pick the most logical spot and take out 1 or 2 deg timing. You won't notice maybe 1 or 2deg timing but it will make a bit of a difference if its knocking under load.
By the temp you mean Airtemp under MONITOR?
The FC has default retarding based on airtemp but its for like 50+deg intake temps, that is, it will take out timing on the whole map when intake temps are over 50 and so on. I think the defaults are 0deg retard for each braket. So if you are seeing intake temps over 50, and its knocking with datalogit we can see your retard for 50deg plus to say -2 and this will cure any knocking (well at least attempt to) when intake temp (AIRTEMP under MONITOR) is over 50deg
You don't need to decrease all the figures at 2400/2800 only on the part of the map thats its knocking.
So its probably somewhere around row 8 or lower on the map window.
Make sure you make a backup of your maps and settings before you start fiddling.
You can write them down or someone with datalogit can copy them for you (i can).